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2PPD
Asym. Unit
Info
Asym.Unit (172 KB)
Biol.Unit 1 (167 KB)
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(1)
Title
:
OXIDIZED H145A MUTANT OF AFNIR BOUND TO NITRIC OXIDE
Authors
:
E. I. Tocheva, M. E. P. Murphy
Date
:
28 Apr 07 (Deposition) - 15 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
H145A, Nitrite Reductase, Nitric Oxide, Denitrification, Bacteria, Oxidoreductase
(Keyword Search:
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)
Reference
:
E. I. Tocheva, F. I. Rosell, A. G. Mauk, M. E. Murphy
Stable Copper-Nitrosyl Formation By Nitrite Reductase In Either Oxidation State
Biochemistry V. 46 12366 2007
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Hetero Components
(5, 10)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: COPPER (I) ION (CU1a)
2b: COPPER (I) ION (CU1b)
2c: COPPER (I) ION (CU1c)
3a: COPPER (II) ION (CUa)
3b: COPPER (II) ION (CUb)
3c: COPPER (II) ION (CUc)
4a: NITRIC OXIDE (NOa)
4b: NITRIC OXIDE (NOb)
5a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
3
CU
3
Ligand/Ion
COPPER (II) ION
2
CU1
3
Ligand/Ion
COPPER (I) ION
4
NO
2
Ligand/Ion
NITRIC OXIDE
5
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:95 , CYS A:136 , MET A:150
BINDING SITE FOR RESIDUE CU1 A 501
02
AC2
SOFTWARE
HIS A:100 , HIS A:135 , NO A:503 , HIS B:306
BINDING SITE FOR RESIDUE CU A 502
03
AC3
SOFTWARE
HIS B:95 , CYS B:136 , MET B:150
BINDING SITE FOR RESIDUE CU1 B 501
04
AC4
SOFTWARE
HIS B:100 , HIS B:135 , NO B:503 , HIS C:306
BINDING SITE FOR RESIDUE CU B 502
05
AC5
SOFTWARE
HIS C:95 , CYS C:136 , MET C:150
BINDING SITE FOR RESIDUE CU1 C 501
06
AC6
SOFTWARE
HIS A:306 , HIS C:100 , HIS C:135 , HOH C:503
BINDING SITE FOR RESIDUE CU C 502
07
AC7
SOFTWARE
GLY B:229 , HIS B:319
BINDING SITE FOR RESIDUE ACT B 1503
08
AC8
SOFTWARE
ASP A:98 , HIS A:100 , HIS A:135 , CU A:502 , HIS B:255 , ILE B:257 , HIS B:306
BINDING SITE FOR RESIDUE NO A 503
09
AC9
SOFTWARE
ASP B:98 , HIS B:100 , HIS B:135 , CU B:502 , HIS C:255 , ILE C:257 , HIS C:306
BINDING SITE FOR RESIDUE NO B 503
10
BC1
SOFTWARE
THR A:212 , LEU A:213 , THR A:214 , HOH A:1633 , HOH A:1667 , HOH A:1671 , THR B:212 , LEU B:213 , THR B:214 , THR C:212 , LEU C:213 , THR C:214
BINDING SITE FOR RESIDUE TRS A 1501
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Sorry, no Info available
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2ppda1 (A:4-166)
1b: SCOP_d2ppda2 (A:167-339)
1c: SCOP_d2ppdb1 (B:4-166)
1d: SCOP_d2ppdb2 (B:167-340)
1e: SCOP_d2ppdc1 (C:4-166)
1f: SCOP_d2ppdc2 (C:167-339)
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Protein Domains
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(
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Organisms
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(
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Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Nitrite reductase, NIR
(79)
Alcaligenes faecalis, strain s-6 [TaxId: 511]
(31)
1a
d2ppda1
A:4-166
1b
d2ppda2
A:167-339
1c
d2ppdb1
B:4-166
1d
d2ppdb2
B:167-340
1e
d2ppdc1
C:4-166
1f
d2ppdc2
C:167-339
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2ppdA01 (A:11-158)
1b: CATH_2ppdB01 (B:11-158)
1c: CATH_2ppdC01 (C:11-158)
1d: CATH_2ppdA02 (A:159-325)
1e: CATH_2ppdB02 (B:159-325)
1f: CATH_2ppdC02 (C:159-325)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Alcaligenes faecalis. Organism_taxid: 511. Strain: s-6.
(24)
1a
2ppdA01
A:11-158
1b
2ppdB01
B:11-158
1c
2ppdC01
C:11-158
1d
2ppdA02
A:159-325
1e
2ppdB02
B:159-325
1f
2ppdC02
C:159-325
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_2ppdC01 (C:174-326)
1b: PFAM_Cu_oxidase_2ppdC02 (C:174-326)
1c: PFAM_Cu_oxidase_2ppdC03 (C:174-326)
2a: PFAM_Cu_oxidase_3_2ppdC04 (C:44-161)
2b: PFAM_Cu_oxidase_3_2ppdC05 (C:44-161)
2c: PFAM_Cu_oxidase_3_2ppdC06 (C:44-161)
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Clans
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Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Alcaligenes faecalis
(18)
1a
Cu-oxidase-2ppdC01
C:174-326
1b
Cu-oxidase-2ppdC02
C:174-326
1c
Cu-oxidase-2ppdC03
C:174-326
Family
:
Cu-oxidase_3
(79)
Alcaligenes faecalis
(18)
2a
Cu-oxidase_3-2ppdC04
C:44-161
2b
Cu-oxidase_3-2ppdC05
C:44-161
2c
Cu-oxidase_3-2ppdC06
C:44-161
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Asym.Unit (172 KB)
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